[R] NADA Package: Referencing Data Frame Columns

[R. Michael Weylandt]

On Tue, Aug 7, 2012 at 11:26 AM, Rich Shepard <rshepard at appl-ecosys.com> wrote:
>   The sample data sets that come with the NADA package are limited to one or
> two variables and a censored measurement indicator column. I try to mimic
> examples using my data but keep missing the target.
>
>   My water chemistry data is available in two formats: long (as seen in a
> database table) and wide (as seen in a spreadsheet). The two structures are:
>
> str(chem)
> 'data.frame':   65349 obs. of  8 variables:
>  $ site    : Factor w/ 64 levels "D-1","D-2","D-3",..: 1 1 1 1 1 1 1 ...
>  $ sampdate: Date, format: "2007-12-12" "2007-12-12" ...
>  $ era     : Factor w/ 2 levels "Post","Pre": 1 1 1 1 1 1 1 1 1 1 ...
>  $ param   : Factor w/ 64 levels "AgDis","AgTot",..: 2 4 5 7 11 15 25 ...
>  $ quant   : num  1.30e-04 1.06e-01 2.31e+02 1.13e-02 5.00e-03 ...
>  $ ceneq1  : logi  TRUE FALSE FALSE FALSE TRUE FALSE ...
>  $ floor   : num  0 0.106 231 0.0113 0 100 0 1.43 0 0.0239 ...
>  $ ceiling : num  1.30e-04 1.06e-01 2.31e+02 1.13e-02 5.00e-03 2.39e-02 ...
>
> and
>
> str(chem.cast)
> 'data.frame':   56938 obs. of  70 variables:
>  $ site     : Factor w/ 64 levels "D-1","D-2","D-3",..: 1 1 1 1 1 ...
>  $ sampdate : Date, format: "2007-12-12" "2007-12-12" ...
>  $ era      : Factor w/ 2 levels "Post","Pre": 1 1 1 1 1 1 1 1 1 1 ...
>  $ ceneq1   : logi  TRUE FALSE FALSE FALSE TRUE FALSE ...
>  $ floor    : num  0 0.106 231 0.0113 0 100 0 1.43 0 0.0239 ...
>  $ ceiling  : num  1.30e-04 1.06e-01 2.31e+02 1.13e-02 5.00e-03 ...
>  $ AgDis    : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ AgTot    : num  0.00013 NA NA NA NA NA NA NA NA NA ...
>  $ AlDis    : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ AlTot    : num  NA 0.106 NA NA NA NA NA NA NA NA ...
>  $ Alk      : num  NA NA 231 NA NA NA NA NA NA NA ...
>  $ AsDis    : num  NA NA NA NA NA NA NA NA NA NA ...
>   and so on.
>
>   I do not know if the latter is appropriate; that is, that the ceneq1,
> floor, and ceiling values are available for each site, sampdate, and
> chemical.
>
>   Is the appropriate way to use the NADA methods for analyses and plotting
> to subset each chemical separately from the 'chem' data frame? Or, is there
> a syntax other than, for example,
>
> cenboxplot(chem&Vdis, chem$ceneq1, chem$era)
> Error in cenros(obs[group == i], cen[group == i]) :
>   error in evaluating the argument 'obs' in selecting a method for function
> 'ros': Error: object 'Vdis' not found
>
>   I get the same error when trying to use the 'chem.cast' data frame.
>


Take a look at with()

Michael

> Rich
>
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